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Author SHA1 Message Date
James A. Fellows Yates
d2b240a17a
Merge branch 'master' into gatk-unifiedgenotyper 2022-06-03 21:24:09 +02:00
James A. Fellows Yates
e827a042ce
Update modules/gatk/unifiedgenotyper/main.nf 
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
 2022-06-03 21:24:03 +02:00
Robert A. Petit III
b534b49b49
Merge pull request #1643 from rpetit3/rp3-add-snippy 
add module for snippy
 2022-06-03 13:20:57 -06:00
Robert A. Petit III
d7cec801b2
Update main.nf 2022-06-03 13:05:43 -06:00
Robert A. Petit III
24ca2ed464
Merge branch 'master' into rp3-add-snippy 2022-06-03 13:01:05 -06:00
Matthias De Smet
24403ce45d
Merge pull request #1707 from matthdsm/bump/picard 
bump picard versions
 2022-06-03 06:39:19 +02:00
Matthias De Smet
cf9d62fc83
Merge branch 'master' into bump/picard 2022-06-02 22:09:42 +02:00
James Fellows Yates
a565d9072a Add GATK UnifiedGenotyper 2022-06-02 21:39:39 +02:00
James Fellows Yates
a14855dbe8 Start meta 2022-06-02 21:22:21 +02:00
James Fellows Yates
544b62df45 Star work on GATK UG 2022-06-02 21:11:17 +02:00
nvnieuwk
fcc186d717
Merge pull request #1728 from nvnieuwk/add-intervals-to-calibratedragstrmodel 
add intervals to gatk4/calibratedragstrmodel
 2022-06-02 16:28:25 +02:00
Nicolas Vannieuwkerke
b028e57588 Merge branch 'add-intervals-to-calibratedragstrmodel' of github.com:nvnieuwk/modules into add-intervals-to-calibratedragstrmodel 2022-06-02 16:24:06 +02:00
Nicolas Vannieuwkerke
f3c0107fa2 added optional to intervals 2022-06-02 16:24:03 +02:00
nvnieuwk
897de827ee
Merge branch 'master' into add-intervals-to-calibratedragstrmodel 2022-06-02 16:20:41 +02:00
Nicolas Vannieuwkerke
b4b1f3b81d add intervals to calibratedragstrmodel 2022-06-02 16:20:12 +02:00
Maxime U. Garcia
3adb54c606
Merge pull request #1727 from maxulysse/master_ensemblvep 
update VEP version + cache
 2022-06-02 16:15:31 +02:00
MaxUlysse
b623ff5d27 fix comments 2022-06-02 16:11:45 +02:00
MaxUlysse
bc0f52bcd3 fix cache version 2022-06-02 16:11:11 +02:00
MaxUlysse
046fa39582 update VEP version + cache 2022-06-02 16:09:09 +02:00
nvnieuwk
59ce1ec348
Merge pull request #1725 from nvnieuwk/add-dragstrmodel-to-haplotypecaller 
add dragstr model to haplotypecaller
 2022-06-02 14:31:53 +02:00
nvnieuwk
e107d61069
Update tests/modules/gatk4/haplotypecaller/test.yml 
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
 2022-06-02 14:20:15 +02:00
nvnieuwk
e419d306df
Update tests/modules/gatk4/haplotypecaller/test.yml 
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
 2022-06-02 14:20:10 +02:00
nvnieuwk
2ce1cf3329
Update tests/modules/gatk4/haplotypecaller/test.yml 
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
 2022-06-02 14:20:04 +02:00
nvnieuwk
a6c4276ad7
Update tests/modules/gatk4/haplotypecaller/test.yml 
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
 2022-06-02 14:19:57 +02:00
Nicolas Vannieuwkerke
e53d091a6d added dragstr model to haplotypecaller 2022-06-02 14:08:09 +02:00
nvnieuwk
5447395975
Merge pull request #1724 from nvnieuwk/new-module-gatk4/CalibrateDragstrModel 
new module gatk4/calibratedragstrmodel
 2022-06-02 13:49:44 +02:00
Matthias De Smet
db0dc81b81
Merge branch 'master' into bump/picard 2022-06-02 13:49:03 +02:00
nvnieuwk
a339f9818a
Merge branch 'master' into new-module-gatk4/CalibrateDragstrModel 2022-06-02 13:42:56 +02:00
Matthias De Smet
22885ce687
Merge pull request #1723 from matthdsm/update/untar 
fix untar output dir
 2022-06-02 13:42:46 +02:00
nvnieuwk
4b430e8ece
Merge branch 'master' into new-module-gatk4/CalibrateDragstrModel 2022-06-02 13:41:20 +02:00
nvnieuwk
3a49b82863
Update modules/gatk4/calibratedragstrmodel/main.nf 
Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
 2022-06-02 13:39:44 +02:00
Matthias De Smet
f58771c47f
Merge branch 'master' into update/untar 2022-06-02 13:38:53 +02:00
SusiJo
1c33eeb348
Merge pull request #1719 from SusiJo/cnvkit_bam 
Adjusted CNVKIT/BATCH for germline mode
 2022-06-02 13:36:39 +02:00
Nicolas Vannieuwkerke
631bf7749a Merge branch 'new-module-gatk4/CalibrateDragstrModel' of github.com:nvnieuwk/modules into new-module-gatk4/CalibrateDragstrModel 2022-06-02 13:22:57 +02:00
Nicolas Vannieuwkerke
d3874bbae9 linting 2022-06-02 13:22:55 +02:00
nvnieuwk
eadab8e002
Merge branch 'master' into new-module-gatk4/CalibrateDragstrModel 2022-06-02 13:18:36 +02:00
Nicolas Vannieuwkerke
2a45d42868 added the calibratedragstrmodel module 2022-06-02 13:17:06 +02:00
SusiJo
2f3ddc90fb added fasta_fai as input + changed if statements 2022-06-02 12:57:50 +02:00
Matthias De Smet
45f3795670
Merge branch 'master' into bump/picard 2022-06-02 11:33:26 +02:00
Matthias De Smet
51be617b1c fix untar output dir 2022-06-02 11:09:55 +02:00
SusiJo
7742661784 Merge remote-tracking branch 'upstream/master' into cnvkit_bam 2022-06-02 10:51:43 +02:00
SusiJo
3294def3fd
Merge pull request #1722 from SusiJo/deeptools_samtools 
Adjust deeptools/bamcoverage with new mulled container
 2022-06-02 10:50:05 +02:00
SusiJo
a21cfb666e changed container + add cram2bam conversion 2022-06-02 10:38:05 +02:00
SusiJo
9fc9be3e7b Merge remote-tracking branch 'origin/master' into cnvkit_bam 2022-06-01 17:35:47 +02:00
SusiJo
f6953b5147 adjust cnvkit/batch for germline mode 2022-06-01 17:35:02 +02:00
nvnieuwk
95e8afe627
Merge pull request #1714 from nvnieuwk/new-module-gatk4/ComposeSTRTableFile 
added gatk4/composestrtablefile
 2022-06-01 09:33:08 +02:00
Nicolas Vannieuwkerke
114a54c8d5 spaces fix 2022-06-01 09:22:09 +02:00
Nicolas Vannieuwkerke
8470f3cb7e linting 2022-06-01 09:20:20 +02:00
Nicolas Vannieuwkerke
d4f3df4677 Updated the test 2022-06-01 09:17:05 +02:00
nvnieuwk
5b74a179c3
Update modules/gatk4/composestrtablefile/main.nf 
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
 2022-06-01 09:14:08 +02:00